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Yorodumi- PDB-7sq0: Get3 bound to ADP and the transmembrane domain of the tail-anchor... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7sq0 | ||||||
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Title | Get3 bound to ADP and the transmembrane domain of the tail-anchored protein Bos1 | ||||||
Components |
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Keywords | CHAPERONE / Tail-anchored membrane protein targeting Deviant Walker A ATPase targeting factor | ||||||
Function / homology | Function and homology information Hydrolases; Acting on acid anhydrides / protein insertion into ER membrane / endoplasmic reticulum / ATP hydrolysis activity / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Giardia intestinalis (eukaryote) Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||
Authors | Fry, M.Y. / Maggiolo, A.O. / Clemons Jr., W.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Struct Mol Biol / Year: 2022 Title: Structurally derived universal mechanism for the catalytic cycle of the tail-anchored targeting factor Get3. Authors: Michelle Y Fry / Vladimíra Najdrová / Ailiena O Maggiolo / Shyam M Saladi / Pavel Doležal / William M Clemons / Abstract: Tail-anchored (TA) membrane proteins, accounting for roughly 2% of proteomes, are primarily targeted posttranslationally to the endoplasmic reticulum membrane by the guided entry of TA proteins (GET) ...Tail-anchored (TA) membrane proteins, accounting for roughly 2% of proteomes, are primarily targeted posttranslationally to the endoplasmic reticulum membrane by the guided entry of TA proteins (GET) pathway. For this complicated process, it remains unknown how the central targeting factor Get3 uses nucleotide to facilitate large conformational changes to recognize then bind clients while also preventing exposure of hydrophobic surfaces. Here, we identify the GET pathway in Giardia intestinalis and present the structure of the Get3-client complex in the critical postnucleotide-hydrolysis state, demonstrating that Get3 reorganizes the client-binding domain (CBD) to accommodate and shield the client transmembrane helix. Four additional structures of GiGet3, spanning the nucleotide-free (apo) open to closed transition and the ATP-bound state, reveal the details of nucleotide stabilization and occluded CBD. This work resolves key conundrums and allows for a complete model of the dramatic conformational landscape of Get3. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7sq0.cif.gz | 205.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7sq0.ent.gz | 162.8 KB | Display | PDB format |
PDBx/mmJSON format | 7sq0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7sq0_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 7sq0_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 7sq0_validation.xml.gz | 34.6 KB | Display | |
Data in CIF | 7sq0_validation.cif.gz | 49.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sq/7sq0 ftp://data.pdbj.org/pub/pdb/validation_reports/sq/7sq0 | HTTPS FTP |
-Related structure data
Related structure data | 25373MC 7spyC 7spzC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 39164.922 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Giardia intestinalis (strain ATCC 50803 / WB clone C6) (eukaryote) Strain: ATCC 50803 / WB clone C6 / Gene: GL50803_7953 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Nico21(DE3) References: UniProt: A8B3G9, Hydrolases; Acting on acid anhydrides #2: Protein | | Mass: 15860.031 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Nico21(DE3) #3: Chemical | #4: Chemical | ChemComp-ZN / | #5: Chemical | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Molecular weight |
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||
Specimen | Conc.: 0.73 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: DARK FIELD / Nominal magnification: 105000 X / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 1.82 sec. / Electron dose: 63.2 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 2732 |
EM imaging optics | Energyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV |
-Processing
Software | Name: PHENIX / Version: 1.16_3549: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1790962 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 70330 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 84.72 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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